The Queen took a tour of Jamestown, Virginia, on Friday as part of the commemorations of its 400th anniversary. The site of England's first permanent colony in North America, recently uncovered in a series of spectacular archaeological excavations, is of huge historical importance. It is the reason the US is an English-speaking nation, with Anglo-Saxon legal, commercial and political institutions. However, the Queen will be not be present for the anniversary itself, which falls this weekend. The reason is a prior commitment that necessitated her presence in the US a week early: the Kentucky Derby, held last Saturday.

The Queen's desire to escape to the safety of the world of horse racing is understandable. Compared to a punt even on a rank outsider, commemorating the arrival of a motley crew of 100 or so English renegades and outcasts on the shores of the Chesapeake Bay in 1607 has proved to be fraught with risk. Not only is there the solemn complication of the campus shootings at nearby Virginia Tech, but there is the small matter of Jamestown being the birthplace of African slavery, Native American genocide and the global tobacco trade, as well as of North American democracy and free enterprise.

When she went to Virginia 50 years ago, there were no such issues to worry about. It was her first visit to the US as Queen (and only the second by a reigning British monarch since the American Revolution, her father's in 1939 being the first), and she received a welcome even more rapturous than Helen Mirren's at the Oscars. At a time when the cold war was at its most intense - with Sputnik, launched by the USSR days before her arrival, circling threateningly overhead - her presence cemented the theme of the 350th anniversary: the celebration of Anglo-Saxon values, or the role of "English-speaking peoples in guarding the basic rights of men", as Thomas Stanley, Virginia's governor, put it.

The visit was a triumph. For some, it was a model of how national anniversaries should be marked, in a robustly patriotic mood, free of moral relativism and political correctness. But that, of course, was achieved by ruthlessly excising complicating or compromising factors. The scene had been set some weeks before the Queen's arrival. At a commemorative dinner hosted by Governor Stanley in Virginia's state capital, Richmond, seven of the "distinguished sons and daughters of the Old Dominion" invited to attend found themselves unceremoniously excluded when it was discovered they were black. Meanwhile, in Jamestown the festivities got under way without a Native American in sight, the only hint being a white drama teacher from a local school dressed as Pocahontas.

Fifty years on, the picture is very different. When the Queen arrived in Richmond on Thursday, she could barely move for Native Americans, meeting representatives of each of Virginia's eight tribes, before moving on to make a speech in which she endorsed "the 'melting pot' metaphor" as capturing "one of the great strengths" of the modern US.

As for the anniversary of Jamestown itself, the word celebration has been banned. Instead we have "America's Anniversary Weekend", in the hope that what sounds like a wholesome family outing will create the right melting pot mood. James Earl Jones has duly been invited to perform, Chaka Kahn to sing, and the Richmond Indigenous Gourd Orchestra (who grow their own instruments) to play.

Meanwhile, the darker, more complex dimensions of the Jamestown story have if anything flourished. The way the colonists treated Native Americans, the importing of Angolans pirated from Portuguese slave ships, the exploitation of the land to grow tobacco, the chronic infighting that nearly destroyed the settlement in its first months - these have become potent elements in attempts to make sense of the combination of high principles and base motives that are such a feature of American history - no more so than the country's recent history of engagement with the Middle East.

As a result, a theme that is not usually much in evidence around the time of national anniversaries has made an unexpected appearance in Virginia: history. There has been an outpouring of books (to which I have contributed), films and articles about those first English settlers. The result has been a profound shift of understanding - unseating, at least for the moment, those pious latecomers the Pilgrim Fathers (the Mayflower arrived in North America 13 years after the Jamestown settlers) from their privileged perch. Despite its faults - perhaps because of them - Jamestown has, at last, emerged as the birthplace of America.

· Benjamin Woolley is the author of Savage Kingdom: Virginia and the Founding of English America Savagekingdom.org